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Yorodumi- PDB-5odo: Crystal Structure of the Oleate hydratase of Rhodococcus erythropolis -
+Open data
-Basic information
Entry | Database: PDB / ID: 5odo | ||||||
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Title | Crystal Structure of the Oleate hydratase of Rhodococcus erythropolis | ||||||
Components | Isomerase | ||||||
Keywords | LYASE / Hydratase / Rossmann fold / FAD binding / fatty acid / immune system | ||||||
Function / homology | oleate hydratase activity / Oleate hydratase / MCRA family / FAD binding / isomerase activity / fatty acid metabolic process / FAD/NAD(P)-binding domain superfamily / FORMIC ACID / Isomerase Function and homology information | ||||||
Biological species | Rhodococcus erythropolis DN1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å | ||||||
Authors | Driller, R. / Lorenzen, J. / Waldow, A. / Qoura, F. / Brueck, T. / Loll, B. | ||||||
Citation | Journal: Chemcatchem / Year: 2017 Title: Rhodococcus erythropolis Oleate Hydratase: a New Member in the Oleate Hydratase Family Tree - Biochemical and Structural Studies. Authors: Lorenzen, J. / Driller, R. / Waldow, A. / Quora, F. / Loll, B. / Brueck, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5odo.cif.gz | 233.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5odo.ent.gz | 186.2 KB | Display | PDB format |
PDBx/mmJSON format | 5odo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5odo_validation.pdf.gz | 453.3 KB | Display | wwPDB validaton report |
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Full document | 5odo_full_validation.pdf.gz | 460.1 KB | Display | |
Data in XML | 5odo_validation.xml.gz | 41.7 KB | Display | |
Data in CIF | 5odo_validation.cif.gz | 60.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/5odo ftp://data.pdbj.org/pub/pdb/validation_reports/od/5odo | HTTPS FTP |
-Related structure data
Related structure data | 4ia5S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 66031.094 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus erythropolis DN1 (bacteria) Gene: N601_10635 / Production host: Escherichia coli (E. coli) / References: UniProt: T5I9M6*PLUS #2: Chemical | #3: Chemical | ChemComp-FMT / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.77 Å3/Da / Density % sol: 74.19 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 100 mM Bis-Tris/HCl 300 mM Magnesium formate 5% (v/v) glycerol PH range: 5.5 - 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.98141 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2016 |
Radiation | Monochromator: SI111-DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98141 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→50 Å / Num. obs: 75230 / % possible obs: 99.8 % / Redundancy: 22.2 % / Net I/σ(I): 13.66 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ia5 Resolution: 2.64→49.466 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.96
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.64→49.466 Å
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Refine LS restraints |
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LS refinement shell |
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